Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate BPHYT_RS34945 BPHYT_RS34945 3-ketoacyl-ACP reductase
Query= SwissProt::Q92RN6 (256 letters) >FitnessBrowser__BFirm:BPHYT_RS34945 Length = 255 Score = 148 bits (374), Expect = 9e-41 Identities = 85/246 (34%), Positives = 138/246 (56%), Gaps = 5/246 (2%) Query: 11 LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70 L R VLVTGG G+GAA V + + GA+V F D+ E AL + Q G A ++ Sbjct: 9 LNGRRVLVTGGARGLGAAFVRSLVQAGAQVVFGDVLHEEGRALAASLVEQ-GHAVTYVPL 67 Query: 71 DLRNVEAVRAAADEAVAKLGSVRVLVNNAA--RDDRQALEAVTEESWDESLSVNLRHLFF 128 DL + +++ A++ A+LG + L+NNAA + + ++ ++WD ++VN+R + Sbjct: 68 DLADPTSIKQFAEQGAAQLGGLDALINNAAITNSGGKFADELSVDTWDAVMNVNVRGTWL 127 Query: 129 MCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRV 188 M A P+++ G GSIVN +S + P++ AY +K +I +T+SLA + G + V Sbjct: 128 MSTAALPYLRDSGRGSIVNIASDTAMWGAPKLLAYVASKGAVISMTRSLAREFGAHQVTV 187 Query: 189 NAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQA 248 NAI PG+ TE + ++ E + + L R V DD+ GP LFL SD++ +T Q Sbjct: 188 NAIAPGL--TEVEATAYVPAERHEYYLQGRALTRAQVPDDVTGPVLFLLSDAARFVTGQL 245 Query: 249 MIIDGG 254 + ++GG Sbjct: 246 LPVNGG 251 Lambda K H 0.321 0.133 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 127 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 256 Length of database: 255 Length adjustment: 24 Effective length of query: 232 Effective length of database: 231 Effective search space: 53592 Effective search space used: 53592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory